Background. The quality of rapeseed oil depends to a considerable degree on raw material quality. Negligence in maintaining the appropriate conditions during long-term rapeseed storage (excessively high humidity and temperature) may contribute to a deterioration of seed quality, as a result of microbial growth and changes in native antioxidant contents. The aim of this study was to investigate the effect of inappropriate storage conditions on changes in sinapic acid derivative content, which is the main phenolic compound in rapeseeds. Material and methods. The material used for tests was canola cv. PR 46 W14. Seeds with a 13.5% moisture content were stored for 21 days in a thermo-hygrostat chamber, ensuring rapeseed storage under constant humidity and temperature conditions. In this study, the level of mould fungi was analysed using the plate method, while those of sinapic acid derivatives were determined using the HPLC-DAD method. Results. Intensive growth of mould fungi in the rapeseeds was observed after 6 days of storage. Changes were recorded in sinapic acid derivative contents, which are the main phenolic compounds in rapeseed. The level of phenolic compounds found in the bound form (sinapin; sinapic acid methyl ester; 1,2-disinapoyldihexoside; 1,2-disinapoyl-hexoside and 1,2,2'-trisinapoyl-dihexoside) decreased. At the same time, an increase was recorded in trans-sinapic acid content (by 63%). Conclusion. Both qualitative and quantitative changes in phenolic compounds may be connected with the development of fungal microflora in stored rapeseeds. Only adequate storage conditions for the oil raw material, such as rapeseeds, may ensure good quality in the final product, in this case, rapeseed oil.